IndexError: list index out of range

[aistBMRG]

Hi,

When running atropos detect, I am experiences issues for some files; as follows:

Run1Sam03_S3_R1_001.fastq.gz 2019-05-20 12:17:34,008 INFO: This is Atropos 1.1.21 with Python 3.6.7 2019-05-20 12:17:34,011 INFO: Detecting adapters and other potential contaminant sequences based on 12-mers in 10000 reads 2019-05-20 12:17:38,409 ERROR: Unknown error Traceback (most recent call last): File "/Volumes/mikami/bio/apps/12.04/sw/atropos/1.1.21/lib/python3.6/site-packages/atropos/util/init.py", line 727, in run_interruptible func(*args, kwargs) File "/Volumes/mikami/bio/apps/12.04/sw/atropos/1.1.21/lib/python3.6/site-packages/atropos/commands/base.py", line 32, in call self.finish(command_runner.summary, kwargs) File "/Volumes/mikami/bio/apps/12.04/sw/atropos/1.1.21/lib/python3.6/site-packages/atropos/commands/detect/init.py", line 481, in finish for match in self.read1_detector.matches(kwargs) File "/Volumes/mikami/bio/apps/12.04/sw/atropos/1.1.21/lib/python3.6/site-packages/atropos/commands/detect/init.py", line 373, in matches self._filter_and_sort(kwargs) File "/Volumes/mikami/bio/apps/12.04/sw/atropos/1.1.21/lib/python3.6/site-packages/atropos/commands/detect/init.py", line 390, in _filter_and_sort matches = self._get_contaminants() File "/Volumes/mikami/bio/apps/12.04/sw/atropos/1.1.21/lib/python3.6/site-packages/atropos/commands/detect/init.py", line 617, in _get_contaminants cur = results[0] IndexError: list index out of range

My command line is as follows:

for x in R1_001.fastq.gz; do atropos detect --no-default-contaminants --no-cache-contaminants -pe1 ${x%%}_SR1_001.fastq.gz -pe2 ${x%%}_SR2_001.fastq.gz --detector heuristic --max-reads 1000000 --output ${x%%}_atropos.txt done

Would it be clarify the source of this issue?

Thank you.

Dieter

[aistBMRG]

sorry, command was as follows:

for x in _R1001.fastq.gz; do atropos detect \ --no-default-contaminants --no-cache-contaminants \ -pe1 ${x%%}_S_R1001.fastq.gz \ -pe2 ${x%%}_S_R2001.fastq.gz \ --detector heuristic \ --output ${x%%}_atropos.txt done

[jdidion]

Thanks for reporting. This should be fixed in 1.1.22.